This page indicates the publications related to the ERC project published after 2010 included.


Y.-P. Deni´lou, F. Boyer, M.-F. Sagot, A. Viari. Multiple alignment of biological networks: A flexible approach. in Combinatorial Pattern Matching 2009, Lecture Notes in Computer Science, volume 5542, pages 173-185, 2009.

V. Acuña, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie. A note on the complexity of finding and enumerating elementary modes. BioSystems, 99(3):210-214, 2010.

C. Baudet, C. Lemaitre, D. Zanoni, C. Gautier, E. Tannier, M.-F. Sagot. Cassis: precise detection of rearrangement breakpoints, Bioinformatics, 26(15):1897-1898, 2010.

L. Cottret, P.V. Milreu, V. Acuña, A. Marchetti-Spaccamela, L. Stougie, H. Charles, M.-F. Sagot. Graph based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata, PLoS Computational Biology, 6(9):307-316, 2010.

N. Mendes, A.T. Freitas, A.T. Vasconcelos, M.-F. Sagot. Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi, BMC Genomics, 11:529, 2010.

Y.-P. Deniélou, M.-F. Sagot, F. Boyer, A. Viari. Bacterial syntenies: An exact approach with gene quorum, BMC Bioinformatics, 12:193, 2011.

P. Simões, G. Mialdea, D. Reiss, M.-F. Sagot, S. Charlat. Wolbachia detection: An assessment of standard PCR Protocols. Molecular Ecology Resources, 11:567-572, 2011.

A.F. Vellozo, A. Véron, P. Baa-Puyoulet, J. Huerta-Cepas, L. Cottret, G. Febvay, F. Calevro, Y. Rahbé, A.E. Douglas, T. Gabaldon, M.-F. Sagot, H. Charles, S. Colella. CycADS: An annotation database system to ease the development and update of BioCyc databases, Database, in press, 2011.


I. Nor, D. Hermelin, S. Charlat, J. Engelstadter, M. Reuter, O. Duron, M.-F. Sagot. Mod/Resc Parsimony Inference. in Combinatorial Pattern Matching 2010, Lecture Notes in Computer Science, vol. 6129, pages 202-213, 2010.

P. Milreu, V. Acuña, E. Birmelé, P. Crescenzi, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie and V. Lacroix Enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms. WABI'2010, LNBI/LNCS, vol. 6293, pages 226-237, 2010.

P. Peterlongo, N. Schnel, N. Pisanti, M.-F. Sagot, V. Lacroix. Identifying SNPs without a reference genome by comparing raw reads, SPIRE, Lecture Notes in Computer Science, vol. 6393, pp.147-158, 2011.

Workshop without proceedings

V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. Milreu, M.-F. Sagot, L Stougie. Telling stories. Workshop of ICALP Graph Algorithms and Applications, 2011.

PhD manuscript

V. Acuña. Models and algorithms for metabolic networks: elementary modes and precursor sets. Reviewers: Pierluigi Crescenzi (Univ. Florence, Italy) and Khaled Elbassioni (Max-Planck Saarbrücken, Germany), PhD supervisors: Marie-France Sagot and Christian Gautier.

N. Mendes. Efficient algorithms for the identification of miRNA motifs in DNA sequences, Reviewers: Christine Gaspin (MIA-INRA Toulouse, France) and Ana Maria Pires Parente (Departement Mathematics, Instituto Superior Técnico Lisbon, Portugal), PhD supervisors: Marie-France Sagot and Ana Teresa Freitas (INESC-ID, Lisbon, Portugal).


I. Nor, S. Charlat, M.-F. Sagot. Boolean matrix decomposition into rectangles and completing sets, 2010.

I. Nor, D. Hermelin, S. Charlat, J. Engelstadter, M. Reuter, O. Duron, M.-F. Sagot. Mod/Resc Parsimony Inference: Theory and Application, 2011.

N. Mendes, S. Heyne, A.T. Freitas, M.-F. Sagot, R. Backofen. Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches, 2011.

C. Klein, L. Cottret, H. Charles, C. Gautier, A.T. Vasconcelos, V. Lacroix, M.-F. Sagot. Absence of a core metabolic network common to symbiotic bacteria, 2011.

In preparation

P. Milreu, V. Acuña, E. Birmelé, A. Marino, L. Cottret, V. Lacroix, A. Marchetti-Spaccamela, L. Stougie, F. Jourdan, M.-F. Sagot, P. Crescenzi. Telling metabolic stories (tentative title).

V. Acuña, P. Milreu, L. Cottret, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot. Enumerating all minimal metabolic precursor sets: complexity analysis and efficient network compression algorithm (tentative title).

Freire A, et al. Covering reactions of a metabolic network by elementary modes (tentative title).